Model and computer simulations of the motion of DNA molecules during pulse field gel electrophoresis.
Model and computer simulations of the motion of DNA molecules during pulse field gel electrophoresis.
复制标题
脉冲场凝胶电泳过程中 DNA 分子运动的模型和计算机模拟。
DOI：
10.1021/bi00235a021
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发表时间：
1991
期刊：
影响因子：
2.9
通讯作者：
Bustamante,C
中科院分区：
文献类型：
--
作者：
Smith,SB;Heller,C;Bustamante,C
摘要：提出了一种脉冲场凝胶电泳法(PFGE)中DNA分子运动的模型。分子由一串由熵弹簧连接的带电珠子表示，凝胶由围绕珠子的分段管子表示。该模型与早期的旋转/管道模型的不同之处在于，允许管道在某些地方泄漏，链条可以折叠并以扭结的形式流出管道的一侧。研究发现，这些扭结经常导致U形的形成，而U形是PFGE中延迟的一个主要来源。将该模型的计算机模拟结果与实际DNA实验结果进行了比较，包括荧光显微镜下的稳态场运动、稳态场中的迁移率、横场交替凝胶电泳法中的迁移率、场反转凝胶电泳法中的迁移率以及琼脂糖凝胶中DNA在PFGE过程中的线性二色性。模拟结果与实验结果吻合较好。里尔斯场凝胶电泳法(PFGE)是一种广泛使用的按大小分离DNA大分子的方法。通常使用两种不同类型的PFGE。第一种类型是从最初的发明(Schwartz&Cantor，1984)发展而来的，现在使用均匀的(非发散的)电场，这种电场周期性地穿过某个钝角
Revised Manuscript Received February 19, 1991 abstract: A model is presented for the motion of individual molecules of DNA undergoing pulse field gel electrophoresis (PFGE). Themolecule is represented by a chain of charged beads connected by entropic springs, and the gelis representedby a segmented tube surrounding the beads. This model differs from earlier reptation/tube models in that the tube is allowed to leak in certain places andthe chain can double over and flow out of the side of the tube in kinks. It is found that these kinks often lead to the formation of U shapes, which are a major source of retardation in PFGE. The results of computer simulations using this model are compared with real DNA experimental results for the following cases: steady field motion as seen in fluorescence microscopy, mobility in steady fields, mobility in transverse field alternation gel electrophoresis (TFAGE), mobility in field inversion gel electrophoresis (FIGE), and linear dichroism (LD) of DNA in agarosegels during PFGE. Good agreement between the simulations and the experimental results is obtained.! Rilse field gel electrophoresis (PFGE) is a widely used method for separating large DNA molecules by size. Two different types of PFGE are commonly used. The first type has evolved from the original invention (Schwartz & Cantor, 1984) and now uses homogeneous (nondivergent) electric fields that are periodically tacked through some obtuse angle with